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(-) Description

Title :  CRYSTAL STRUCTURE OF URONATE ISOMERASE (TM0064) FROM THERMOTOGA MARITIMA AT 2.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Jul 02  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Tm0064, Uronate Isomerase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Schwarzenbacher, J. M. Canaves, L. S. Brinen, X. Dai, A. M. Deacon, M. A. Elsliger, S. Eshaghi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, C. Guda, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley, D. Mcmullan, T. M. Mcphillips, M. A. Miller, M. D. Miller, A. Morse, K. Moy, J. Ouyang, A. Robb, K. Rodrigues, T. L. Selby, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of Uronate Isomerase (Tm0064) From Thermotoga Maritima At 2. 85 A Resolution.
Proteins V. 53 142 2003
PubMed-ID: 12945057  |  Reference-DOI: 10.1002/PROT.10462
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URONATE ISOMERASE
    Chains: A, B, C
    EC Number: 5.3.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0064
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: GLUCURONATE ISOMERASE, URONIC ISOMERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J5S)

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1SAAUTHORHIS A:30 , HIS A:32 , TRP A:366 , ASP A:397 , HOH A:452ACTIVE SITE AT H30, H32, W366, D397. THESE RESIDUES COORDINATE A PUTATIVE METAL ION WHICH HAS BEEN MODELED AS WATER 1 (CHAIN A).
2SBAUTHORHIS B:30 , HIS B:32 , TRP B:366 , ASP B:397 , HOH B:452ACTIVE SITE AT H30, H32, W366, D397. THESE RESIDUES COORDINATE A PUTATIVE METAL ION WHICH HAS BEEN MODELED AS WATER 2 (CHAIN B).
3SCAUTHORHIS C:30 , HIS C:32 , TRP C:366 , ASP C:397 , HOH C:452ACTIVE SITE AT H30, H32, W366, D397. THESE RESIDUES COORDINATE A PUTATIVE METAL ION WHICH HAS BEEN MODELED AS WATER 3 (CHAIN C).

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J5S)

(-) Exons   (0, 0)

(no "Exon" information available for 1J5S)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:451
 aligned with UXAC_THEMA | Q9WXR9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:451
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449 
           UXAC_THEMA     - -MFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
               SCOP domains d1j5sa_ A: Uronate isomerase TM0064                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -1j5sA01 A:1-42,A:134-450                  1j5sA02 A:43-133 uronate isomerase, domain 2, chain A                                      1j5sA01 A:1-42,A:134-450 Metal-dependent hydrolases                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh...eee.....hhhhhhhh....hhhhhhh..hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhh.eeeee........hhhhhhhhhhh...eee....hhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.ee...hhhhhhhh.......ee....hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j5s A   0 HMFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449 


Chain B from PDB  Type:PROTEIN  Length:450
 aligned with UXAC_THEMA | Q9WXR9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           UXAC_THEMA     1 MFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
               SCOP domains d1j5sb_ B: Uronate isomerase TM0064                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j5sB01 B:1-42,B:134-450                  1j5sB02 B:43-133 uronate isomerase, domain 2, chain A                                      1j5sB01 B:1-42,B:134-450 Metal-dependent hydrolases                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh...eee.....hhhhhhhh....hhhhhhh..hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhh.eeeee........hhhhhhhhhhh...eee....hhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.ee...hhhhhhhh.......ee....hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j5s B   1 MFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450


Chain C from PDB  Type:PROTEIN  Length:450
 aligned with UXAC_THEMA | Q9WXR9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
           UXAC_THEMA     1 MFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
               SCOP domains d1j5sc_ C: Uronate isomerase TM0064                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1j5sC01 C:1-42,C:134-450                  1j5sC02 C:43-133 uronate isomerase, domain 2, chain A                                      1j5sC01 C:1-42,C:134-450 Metal-dependent hydrolases                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh...eee.....hhhhhhhh....hhhhhhh..hhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhh.eeeee........hhhhhhhhhhh...eee....hhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee.ee...hhhhhhhh.......ee....hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhh..hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j5s C   1 MFLGEDYLLTNRAAVRLFNEVKDLPIVDPHNHLDAKDIVENKPWNDIWEVEGATDHYVWELMRRCGVSEEYITGSRSNKEKWLALAKVFPRFVGNPTYEWIHLDLWRRFNIKKVISEETAEEIWEETKKKLPEMTPQKLLRDMKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVDKEGWREYVEKMGERYGEDTSTLDGFLNALWKSHEHFKEHGCVASDHALLEPSVYYVDENRARAVHEKAFSGEKLTQDEINDYKAFMMVQFGKMNQETNWVTQLHIGALRDYRDSLFKTLGPDSGGDISTNFLRIAEGLRYFLNEFDGKLKIVLYVLDPTHLPTISTIARAFPNVYVGAPWWFNDSPFGMEMHLKYLASVDLLYNLAGMVTDSRKLLSFGSRTEMFRRVLSNVVGEMVEKGQIPIKEARELVKHVSYDGPKALFF 450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J5S)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (UXAC_THEMA | Q9WXR9)
molecular function
    GO:0008880    glucuronate isomerase activity    Catalysis of the reaction: D-glucuronate = D-fructuronate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006064    glucuronate catabolic process    The chemical reactions and pathways resulting in the breakdown of glucuronate, any salt or ester of glucuronic acid.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1J5S)

(-) Related Entries Specified in the PDB File

1a4m TM0064 IS HOMOLOGOUS TO ENTRY 1A4M AND SHARES 13% SEQUENCE IDENTITY IN 218 RESIDUES. RELATED ID: 281945 RELATED DB: TARGETDB
1j79 TM0064 IS HOMOLOGOUS TO ENTRY 1J79 AND SHARES 11% SEQUENCE IDENTITY IN 223 RESIDUES.
1k6w TM0064 IS HOMOLOGOUS TO ENTRY 1K6W AND SHARES 10% SEQUENCE IDENTITY IN 221 RESIDUES.
1psc TM0064 IS HOMOLOGOUS TO ENTRY 1PSC AND SHARES 10% SEQUENCE IDENTITY IN 235 RESIDUES.
1upb TM0064 IS HOMOLOGOUS TO ENTRY 1UPB AND SHARES 10% SEQUENCE IDENTITY IN 219 RESIDUES.